Amino Acid Properties Reference: Molecular Weight, Side-Chain pKa, Hydrophobicity, and Codon Count
Molecular weight, side-chain pKa, hydrophobicity, and codon count for all 20 standard amino acids. Browse the table directly, or use the search box to look up a single amino acid by one-letter code, three-letter code, or name.
Properties of the 20 amino acids
| Name | 3-letter | 1-letter | Residue mass (Da) | Free MW (Da) | Side-chain pKa | Hydropathy (KD) | Codons |
|---|---|---|---|---|---|---|---|
| Alanine | Ala | A | 71.0788 | 89.09 | — | +1.8 | 4 |
| Arginine | Arg | R | 156.1875 | 174.20 | 12.5 | -4.5 | 6 |
| Asparagine | Asn | N | 114.1038 | 132.12 | — | -3.5 | 2 |
| Aspartic acid | Asp | D | 115.0886 | 133.10 | 3.9 | -3.5 | 2 |
| Cysteine | Cys | C | 103.1388 | 121.15 | 8.5 | +2.5 | 2 |
| Glutamine | Gln | Q | 128.1307 | 146.15 | — | -3.5 | 2 |
| Glutamic acid | Glu | E | 129.1155 | 147.13 | 4.1 | -3.5 | 2 |
| Glycine | Gly | G | 57.0519 | 75.07 | — | -0.4 | 4 |
| Histidine | His | H | 137.1411 | 155.16 | 6.5 | -3.2 | 2 |
| Isoleucine | Ile | I | 113.1594 | 131.17 | — | +4.5 | 3 |
| Leucine | Leu | L | 113.1594 | 131.17 | — | +3.8 | 6 |
| Lysine | Lys | K | 128.1741 | 146.19 | 10.8 | -3.9 | 2 |
| Methionine | Met | M | 131.1926 | 149.21 | — | +1.9 | 1 |
| Phenylalanine | Phe | F | 147.1766 | 165.19 | — | +2.8 | 2 |
| Proline | Pro | P | 97.1167 | 115.13 | — | -1.6 | 4 |
| Serine | Ser | S | 87.0782 | 105.09 | — | -0.8 | 6 |
| Threonine | Thr | T | 101.1051 | 119.12 | — | -0.7 | 4 |
| Tryptophan | Trp | W | 186.2132 | 204.23 | — | -0.9 | 1 |
| Tyrosine | Tyr | Y | 163.1760 | 181.19 | 10.1 | -1.3 | 2 |
| Valine | Val | V | 99.1326 | 117.15 | — | +4.2 | 4 |
Grouped by side-chain property
| Class | Amino acids |
|---|---|
| Hydrophobic (Kyte-Doolittle > 0) | Alanine(A), Isoleucine(I), Leucine(L), Methionine(M), Phenylalanine(F), Valine(V) |
| Basic (side-chain pKa > 6) | Arginine(R), Histidine(H), Lysine(K) |
| Hydrophilic, non-ionizable side chain | Asparagine(N), Glutamine(Q), Glycine(G), Proline(P), Serine(S), Threonine(T), Tryptophan(W) |
| Acidic (side-chain pKa < 7) | Aspartic acid(D), Glutamic acid(E) |
| Ionizable, mostly uncharged at physiological pH | Cysteine(C), Tyrosine(Y) |
Data Sources
- Residue mass: ExPASy average residue mass. The “free molecular weight” in the table is residue mass plus one water molecule (18.015 Da) — residues in a peptide chain have already lost one water molecule, which is why the two values differ.
- Side-chain pKa: Values from EMBOSS
iep. Only 7 amino acids have ionizable side chains; the rest are marked “—”. - Hydrophobicity: Kyte & Doolittle scale, J. Mol. Biol. 157:105–132 (1982), sourced from ExPASy ProtScale.
- Codon count: NCBI standard genetic code (Table 1).
Two Common Misreadings
The groupings are derived from the data above, not copied from a textbook. Acidic/basic classification follows side-chain pKa; hydrophobic/hydrophilic classification follows the sign of the Kyte-Doolittle value. The rules are stated in the table header. One consequence is results that differ from convention — most notably tryptophan: its KD value is −0.9, which places it on the hydrophilic side by sign, even though it is commonly classified as an aromatic, hydrophobic amino acid. The data are not wrong; hydrophobicity scales genuinely disagree, and tryptophan, glycine, and proline are the three residues with the greatest inter-scale discrepancy. Switch to a different scale (e.g., Hopp-Woods or Eisenberg) and the ranking changes. Which scale to use depends on what you are trying to explain.
Leucine and isoleucine have identical masses (113.1594 Da); they are structural isomers. Conventional MS/MS cannot distinguish them — specific fragmentation methods such as ETD/EThcD that produce side-chain loss ions are required, a classic headache in proteomics.
FAQ
Why do residue mass and molecular weight differ?
Each amino acid added to a peptide chain loses one water molecule, so residue mass is 18.015 Da less than the free amino acid molecular weight. To calculate a protein's molecular weight, sum the residue masses and add one water molecule — do not add the free molecular weights directly, as that overcounts by 18 Da per residue.
Why do only 7 amino acids have side-chain pKa values?
Only Asp, Glu, His, Cys, Tyr, Lys, and Arg have ionizable groups in their side chains; the remaining side chains do not gain or lose protons in aqueous solution. When calculating isoelectric point, only these 7 residues, plus the N-terminus and C-terminus, contribute to the charge balance.
How are the hydrophobicity values used?
The Kyte-Doolittle scale is most commonly used in sliding-window scans to identify transmembrane helices: a 19-residue window with an average above 1.6 suggests a putative transmembrane segment. Single-residue values have limited meaning on their own — the scale was designed for windowed analysis.
Can leucine and isoleucine really not be distinguished?
Not by conventional MS/MS — they are structural isomers with identical masses (113.1594 Da). Distinguishing them requires side-chain loss ions produced by specific fragmentation methods such as ETD/EThcD. In routine proteomics workflows, they are typically reported as L/I ambiguous.
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